[BioC] Can't load the arabidopsis.db annotation package created in AnnotationDbi

[Groot, Philip de]

Hello Marc,
 
Thank you for updating the libraries! I updated, rebuild, and tested everything and know it all works fine. I updated the Arabidopsis annotation libraries for the MBNI Custom CDF versions 10.0.0 and 11.0.0. These are available for download from: http://nugo-r.bioinformatics.nl/NuGO_R.html.
 
Regards,
 
Dr. Philip de Groot Ph.D.
Bioinformatics Researcher

Wageningen University / TIFN
Nutrigenomics Consortium
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
PO Box 8129, 6700 EV Wageningen
Visiting Address: "De Valk" ("Erfelijkheidsleer"), Building 304
Verbindingsweg 4, 6703 HC  Wageningen
Room: 0052a
T: 0317 485786
F: 0317 483342
E-mail:   Philip.deGroot at wur.nl
Internet: http://www.nutrigenomicsconsortium.nl <http://www.nutrigenomicsconsortium.nl/> 
             http://humannutrition.wur.nl <http://humannutrition.wur.nl/> 
 
 

________________________________

From: Marc Carlson [mailto:mcarlson at fhcrc.org]
Sent: Mon 3-11-2008 21:42
To: Groot, Philip de
Cc: Sean Davis; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Can't load the arabidopsis.db annotation package created in AnnotationDbi



Hi Philip,

This seems to be a small bug in SQLForge that only impacts custom-made
Arabidopsis packages.  I am working on a fix already and should have it
patched up today sometime.  Once I have checked in the changes, you will
have to update both your arabidopsis.db0 package AND AnnotationDbi in
order to get the change.  Also, it may take 24 hours for the build
system to put the new packages online once they have been checked in.


  Marc




Groot, Philip de wrote:
> Oops,
> 
> Sorry, I should have known! Here you have it:
> 
>  
>> library(ath1attair.db)
>>    
> Loading required package: AnnotationDbi
> Loading required package: Biobase
> Loading required package: tools
> Welcome to Bioconductor
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
> Loading required package: DBI
> Error in sqliteExecStatement(con, statement, bind.data) :
>   RS-DBI driver: (error in statement: no such table: chrlengths)
> Error : .onLoad failed in 'loadNamespace' for 'ath1attair.db'
> Error: package/namespace load failed for 'ath1attair.db'
>  
>> sessionInfo()
>>    
> R version 2.8.0 (2008-10-20)
> x86_64-unknown-linux-gnu
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods 
> [8] base    
> other attached packages:
> [1] RSQLite_0.7-0       DBI_0.2-4           AnnotationDbi_1.4.0
> [4] Biobase_2.2.0     
>  
>
> What I think that is going on is that no chrlength information is available and hence the generation of this table is skipped. However, on library load it is still checked whether this table is available...
> 
> Regards,
> 
> Philip
>
> ________________________________
>
> Van: seandavi at gmail.com namens Sean Davis
> Verzonden: ma 3-11-2008 17:16
> Aan: Groot, Philip de
> CC: bioconductor at stat.math.ethz.ch
> Onderwerp: Re: [BioC] Can't load the arabidopsis.db annotation package created in AnnotationDbi
>
>
>
>
> On Mon, Nov 3, 2008 at 11:10 AM, Groot, Philip de <philip.degroot at wur.nl> wrote:
>
>
>       Hello all,
>      
>       I created an arabidopsis library based on the MBNI custom CDF version 10 (TAIR), see http://nugo-r.bioinformatics.nl/NuGO_R.html. In BioC 2.2 all works very well. However, when trying to load the package in R-2.8.0/BioC 2.3, I get the following error message:
>      
>       > library(ath1attair.db)
>       Loading required package: DBI
>       Error in sqliteExecStatement(con, statement, bind.data) :
>        RS-DBI driver: (error in statement: no such table: chrlengths)
>       Error : .onLoad failed in 'loadNamespace' for 'ath1attair.db'
>       Error: package/namespace load failed for 'ath1attair.db'
>      
>      
>       Rebuilding the library with the "makeARABIDOPSISCHIP_DB" function did not solve the problem. The library installs without error message, but fails to load.
>      
>       The error message is obvious (no chrlengths table), but how can I solve this problem?
>      
>
>
> Hi, Philip.  I think you will need to include your sessionInfo() so that folks can see versions of AnnotationDbi, RSQLite, etc.
>
> Sean
>   
>
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